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RNF17 Gene

protein-coding   GIFtS: 48
GCID: GC13P025338

Ring Finger Protein 17

(Previous name: tudor domain containing 4)
(Previous symbol: TDRD4)
  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Ring Finger Protein 171 2     Tudor Domain-Containing Protein 42 3
TDRD41 2 3     Mmip-22
Tudor Domain Containing 41 2     SPATA232
Spermatogenesis Associated 231 2     

External Ids:    HGNC: 100601   Entrez Gene: 561632   Ensembl: ENSG000001329727   OMIM: 6057935   UniProtKB: Q9BXT83   

Export aliases for RNF17 gene to outside databases

Previous GC identifers: GC13P023318 GC13P019318 GC13P024268 GC13P023136 GC13P024236 GC13P006151


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RNF17 Gene:
This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain.
Alternatively spliced transcript variants encoding different isoforms have been found. (provided by RefSeq, May
2010)

GeneCards Summary for RNF17 Gene:
RNF17 (ring finger protein 17) is a protein-coding gene. Diseases associated with RNF17 include type 1 diabetes. GO annotations related to this gene include hydrolase activity, acting on ester bonds and protein homodimerization activity. An important paralog of this gene is TDRD1.

UniProtKB/Swiss-Prot: RNF17_HUMAN, Q9BXT8
Function: Seems to be involved in regulation of transcriptional activity of MYC. In vitro, inhibits DNA-binding
activity of Mad-MAX heterodimers. Can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the
cytoplasm. May be involved in spermiogenesis (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000013.11  NT_024524.15  NC_018924.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RNF17 gene promoter:
         FOXD1   HNF-4alpha2   HNF-4alpha1   E47   Evi-1   GATA-2   RORalpha1   c-Rel   c-Jun   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRNF17 promoter sequence
   Search Chromatin IP Primers for RNF17

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNF17


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 13q12.12   Ensembl cytogenetic band:  13q12.12   HGNC cytogenetic band: 13q12.13

RNF17 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNF17 gene location

GeneLoc information about chromosome 13         GeneLoc Exon Structure

GeneLoc location for GC13P025338:  view genomic region     (about GC identifiers)

Start:
25,338,290 bp from pter      End:
25,454,059 bp from pter
Size:
115,770 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: RNF17_HUMAN, Q9BXT8 (See protein sequence)
Recommended Name: RING finger protein 17  
Size: 1623 amino acids; 184643 Da
Subunit: Interacts with MXD1, MXD3, MXD4, MXI1 and PIWIL1. Self-associates (By similarity)
Sequence caution: Sequence=AAH64847.1; Type=Erroneous initiation; Sequence=BAA91972.1; Type=Erroneous initiation;
1 PDB 3D structure from and Proteopedia for RNF17:
2EQK (3D)    
Secondary accessions: Q5T2J9 Q6P1W3 Q9BXT7 Q9NUY9
Alternative splicing: 5 isoforms:  Q9BXT8-3   Q9BXT8-1   Q9BXT8-2   Q9BXT8-4   Q9BXT8-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RNF17: NX_Q9BXT8

Explore proteomics data for RNF17 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RNF17 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001171922.1  NP_112567.2  

    ENSEMBL proteins: 
     ENSP00000255324   ENSP00000255325   ENSP00000388892   ENSP00000344776   ENSP00000371346  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    TDRD: Tudor domain containing
    RNF: RING-type (C3HC4) zinc fingers

    4 InterPro protein domains:
     IPR017907 Znf_RING_CS
     IPR001841 Znf_RING
     IPR016071 Staphylococal_nuclease_OB-fold
     IPR002999 Tudor

    Graphical View of Domain Structure for InterPro Entry Q9BXT8

    ProtoNet protein and cluster: Q9BXT8

    2 Blocks protein domains:
    IPB001841 Zn-finger
    IPB008191 Maternal tudor protein


    UniProtKB/Swiss-Prot: RNF17_HUMAN, Q9BXT8
    Similarity: Contains 1 RING-type zinc finger
    Similarity: Contains 4 Tudor domains


    RNF17 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RNF17_HUMAN, Q9BXT8
    Function: Seems to be involved in regulation of transcriptional activity of MYC. In vitro, inhibits DNA-binding
    activity of Mad-MAX heterodimers. Can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the
    cytoplasm. May be involved in spermiogenesis (By similarity)

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0005515protein binding ----
    GO:0008270zinc ion binding IEA--
    GO:0016788hydrolase activity, acting on ester bonds IEA--
    GO:0042803protein homodimerization activity IEA--
         
    RNF17 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for RNF17:
     Increased gamma-H2AX phosphory  Synthetic lethal with c-Myc af 

         2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Rnf17):
     endocrine/exocrine gland  reproductive system 

    RNF17 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Rnf17tm1Jw for RNF17

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for RNF17
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RNF17_HUMAN, Q9BXT8: Cytoplasm (By similarity). Nucleus (By similarity). Note=Predominantly found in the
    cytoplasm. Component of a nuage in male germ cells (an electron-dense spherical cytoplasmic body present in late
    pachytene and diplotene spermatocytes and in elonging spermatids) (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    mitochondrion2

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--

    RNF17 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RNF17
    Interactions:

        Search GeneGlobe Interaction Network for RNF17

    STRING Interaction Network Preview (showing 5 interactants - click image to see 13)

    Selected Interacting proteins for RNF17 (Q9BXT82, 3 ENSP000002553244) via UniProtKB, MINT, STRING, and/or I2D (see all 565)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    UBE2UQ5VVX93, ENSP000003601164I2D: score=1 STRING: ENSP00000360116
    CDC5LQ994592, ENSP000003605324MINT-7947479 STRING: ENSP00000360532
    ABCF1Q8NE712MINT-7947479
    ABCF3Q9NUQ82MINT-7947479
    ACTBP607092MINT-7947479
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0007286spermatid development IEA--

    RNF17 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RNF17



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for RNF17 gene (3 alternative transcripts): 
    NM_001184993.1  NM_031277.2  NM_031994.1  

    Unigene Cluster for RNF17:

    Ring finger protein 17
    Hs.97464  [show with all ESTs]
    Unigene Representative Sequence: BC037275
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000255324(uc001upr.3 uc010tde.2 uc010aab.3 uc001ups.3 uc010aac.3 uc010aad.3)
    ENST00000255326(uc001upq.1) ENST00000255325 ENST00000418120 ENST00000339524
    ENST00000381921(uc010tdd.1)
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    Additional mRNA sequence: 

    AK001907.1 AK302405.1 AK302435.1 BC037275.1 BC064847.1 

    6 DOTS entries:

    DT.99934906  DT.105575  DT.100718711  DT.92414307  DT.91752138  DT.100748768 

    Selected AceView cDNA sequences (see all 33):

    CD557770 AA917074 CR618892 BC064847 NM_019038 AI637931 NM_031277 NM_031994 
    AI655402 AF285603 AI807800 AK001907 AF285602 AU156763 CD358307 AI684454 
    BU182455 AA400911 BQ432720 BX378978 BI459805 AU136520 BX093151 BC037275 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RNF17 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTCCAGCAC
    RNF17 Expression
    About this image


    RNF17 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 5) fully expand
     
     NULL (Uncategorized)    fully expand to see all 2 entries
             Short-term differentiated embryoid bodies
     
     Inner Cell Mass (Early Embryonic Tissues)
             ES-J1
     
     Gonad
             XY Germ Cells Testis Cord
     
     Testis (Reproductive System)
             XY Germ Cells Testis Cord
     
     Ovary (Reproductive System)
             XX Germ Cells Ovigerous Cord
    RNF17 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RNF17 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.97464

    UniProtKB/Swiss-Prot: RNF17_HUMAN, Q9BXT8
    Tissue specificity: Testis specific

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for RNF17 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rnf171 , 5 ring finger protein 171, 5 82.47(n)1
    75.89(a)1
      14 (28.21 cM)5
    300541  NM_001033043.11  NP_001028215.11 
     564026975 
    chicken
    (Gallus gallus)
    Aves RNF171 ring finger protein 17 61.97(n)
    50.17(a)
      418961  XM_004938816.1  XP_004938873.1 
    lizard
    (Anolis carolinensis)
    Reptilia RNF176
    ring finger protein 17
    45(a)
    1 ↔ 1
    3(186821149-186905122)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia rnf171 ring finger protein 17 55.4(n)
    43.94(a)
      100490831  XM_002937963.2  XP_002938009.2 
    zebrafish
    (Danio rerio)
    Actinopterygii rnf171 ring finger protein 17 47.13(n)
    35.21(a)
      334519  XM_692362.3  XP_697454.3 
    fruit fly
    (Drosophila melanogaster)
    Insecta tud6
    qin6
    qin
    9(a)
    13(a)
    many ↔ many
    many ↔ many
    2R(17070937-17079903)
    3R(14416749-14475859)


    ENSEMBL Gene Tree for RNF17 (if available)
    TreeFam Gene Tree for RNF17 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RNF17 gene
    TDRD12  TDRD62  TDRD152  TDRD52  

    RNF17 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for RNF17 (see all 2555)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 13 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1507360791,2
    C,Funtested125367402(+) GCATCC/G/TCCTAA 4 S syn12NA EU 5873
    rs578288331,2
    C,F--25336336(+) AACCCA/GGTCAA 2 -- us2k13Minor allele frequency- G:0.10WA NA EA 358
    rs1387148801,2
    --25336415(+) AGACAA/GGAGAA 2 -- us2k10--------
    rs1492759911,2
    --25336426(+) TTGCTG/TGAACC 2 -- us2k10--------
    rs1919514731,2
    --25336432(+) GAACCA/CGGAGA 2 -- us2k10--------
    rs1445343371,2
    C--25336459(+) CTGAGA/TTCTCG 2 -- us2k10--------
    rs1847895781,2
    C--25336486(+) TGGGCA/GACAGA 2 -- us2k10--------
    rs1119593281,2
    C,F--25336508(+) TTTCTT/AAAAAA 2 -- us2k12Minor allele frequency- A:0.50WA NA 4
    rs105344301,2
    C--25336522(+) aaaaa-/AAAAAA
            
    aaaaa
    4 -- us2k1 cds11Minor allele frequency- AAAAAA:0.00NA 2
    rs1893081591,2
    --25336717(+) TAGGGA/CAGCAG 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for RNF17 (25338290 - 25454059 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for RNF17:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2664108CNV Deletion23128226
    esv33422CNV Loss17666407
    nsv899941CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605793    OMIM disorders: --

    1 disease for RNF17:    
    About MalaCards
    type 1 diabetes


    RNF17 for disorders           About GeneDecksing

    Genetic Association Database (GAD): RNF17

    Export disorders for RNF17 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for RNF17 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with RNF17)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. An abundance of X-linked genes expressed in spermatogonia. (PubMed id 11279525)1, 2, 3 Wang P.J.... Page D.C. (Nat. Genet. 2001)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    3. Tudor domain-containing protein 4 as a potential cancer/testis antigen in liver cancer. (PubMed id 21515969)1 Yoon H....Kim H. (Tohoku J. Exp. Med. 2011)
    4. A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose. (PubMed id 19875614)4 Paterson A.D....Bull S.B. (Diabetes 2010)
    5. A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. (PubMed id 19690564)1 van Wijk S.J....Timmers H.T. (Mol. Syst. Biol. 2009)
    6. The DNA sequence and analysis of human chromosome 13. (PubMed id 15057823)2 Dunham A.... Ross M.T. (Nature 2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    9. Androgen-receptor-interacting nuclear proteins. (PubMed id 10961928)1 JAonne O.A....Palvimo J.J. (Biochem. Soc. Trans. 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 56163 HGNC: 10060 AceView: TDRD4andRNF17 Ensembl:ENSG00000132972 euGenes: HUgn56163
    ECgene: RNF17 H-InvDB: RNF17

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RNF17 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for RNF17 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RNF17 gene:
    Search GeneIP for patents involving RNF17

    GeneCards and IP:
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